During one of the cutscenes after Cubot has his body destroyed, Orbot says "Alas, poor Cubot. I knew him well". This is a reference to the often misquoted line from Shakespeare's Hamlet; "Alas, poor Yorick! I knew him, Horatio".

Found within the game data for the Wii U version of the game are files for the Cube and Spike Wisp Powers from Sonic Colors, along with an unused Snake Transformation, none of which appear in either versions of the final release.

There is an unused fanfare sound effect when completing the act or getting a item. This may have been played when the player wasted time, got a game over or got an bad rank. However, the filename was called sys_jingle_release_ng. that ng stand for "Not Good or No Good".

There are gossip stones throughout the Zelda zone included in the Legend of Zelda DLC pack. They respond to the player's actions similarly to how they did in Ocarnia of Time, such as producing a fairy that will heal the player, or blasting off like a rocket if blown up with a bomb.

After the development for Sonic Colors ended, a few members of Sonic Team began experimenting with a new Sonic game. During this time, Sonic Team also planned to build a game which fully utilized the 3DS' various features. Eventually, between the release of Sonic Generations and the announcement of the Wii U, development for a PC version of Sonic Lost World had fully begun. Sega eventually decided it would be best to develop the game for a Nintendo platform, considering Sonic's success on Nintendo consoles, and started to develop a Wii U version of the game, taking advantage of the Wii U's dual-screen capability and Gamepad. Once the basic stage structure and storyline was confirmed, development also began on a 3DS version of the game.